Starting phenix.real_space_refine on Thu Mar 6 01:51:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bpv_44791/03_2025/9bpv_44791.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bpv_44791/03_2025/9bpv_44791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bpv_44791/03_2025/9bpv_44791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bpv_44791/03_2025/9bpv_44791.map" model { file = "/net/cci-nas-00/data/ceres_data/9bpv_44791/03_2025/9bpv_44791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bpv_44791/03_2025/9bpv_44791.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 2819 2.51 5 N 749 2.21 5 O 821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4417 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1613 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "B" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1570 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 19, 'TRANS': 176} Chain: "C" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1206 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.28, per 1000 atoms: 0.74 Number of scatterers: 4417 At special positions: 0 Unit cell: (76.68, 91.59, 101.175, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 821 8.00 N 749 7.00 C 2819 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 188 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 62 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 130 " distance=2.02 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 197 " distance=2.04 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 103 " distance=2.02 Simple disulfide: pdb=" SG CYS C 38 " - pdb=" SG CYS C 136 " distance=2.02 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 162 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 301 " - " ASN B 122 " " NAG B 302 " - " ASN B 9 " Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 525.5 milliseconds 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1048 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 10 sheets defined 26.4% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.556A pdb=" N THR A 111 " --> pdb=" O PRO A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'C' and resid 5 through 11 removed outlier: 3.921A pdb=" N GLN C 8 " --> pdb=" O HIS C 5 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SER C 11 " --> pdb=" O GLN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 34 removed outlier: 4.061A pdb=" N LEU C 33 " --> pdb=" O GLU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 Processing helix chain 'C' and resid 55 through 79 removed outlier: 4.548A pdb=" N VAL C 59 " --> pdb=" O ARG C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 102 removed outlier: 4.363A pdb=" N VAL C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLN C 88 " --> pdb=" O ASP C 84 " (cutoff:3.500A) Proline residue: C 89 - end of helix Processing helix chain 'C' and resid 116 through 128 Processing helix chain 'C' and resid 133 through 144 Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 151 through 159 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 32 removed outlier: 4.311A pdb=" N VAL A 27 " --> pdb=" O GLN A 39 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLN A 39 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N MET A 29 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE A 37 " --> pdb=" O MET A 29 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER A 31 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LYS A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 69 removed outlier: 5.634A pdb=" N GLN A 63 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N SER A 58 " --> pdb=" O GLN A 63 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LYS A 65 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR A 56 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N MET A 67 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA A 54 " --> pdb=" O MET A 67 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N THR A 86 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 69 removed outlier: 5.634A pdb=" N GLN A 63 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N SER A 58 " --> pdb=" O GLN A 63 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LYS A 65 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N TYR A 56 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N MET A 67 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA A 54 " --> pdb=" O MET A 67 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N THR A 86 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 123 Processing sheet with id=AA5, first strand: chain 'A' and resid 167 through 169 Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 15 Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 41 Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 115 Processing sheet with id=AA9, first strand: chain 'B' and resid 150 through 152 Processing sheet with id=AB1, first strand: chain 'B' and resid 150 through 152 191 hydrogen bonds defined for protein. 504 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1380 1.34 - 1.46: 773 1.46 - 1.58: 2343 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 4534 Sorted by residual: bond pdb=" N PHE C 43 " pdb=" CA PHE C 43 " ideal model delta sigma weight residual 1.462 1.494 -0.032 8.50e-03 1.38e+04 1.45e+01 bond pdb=" N VAL A 191 " pdb=" CA VAL A 191 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.14e-02 7.69e+03 1.08e+01 bond pdb=" N VAL A 89 " pdb=" CA VAL A 89 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.14e-02 7.69e+03 1.04e+01 bond pdb=" N VAL C 59 " pdb=" CA VAL C 59 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 9.85e+00 bond pdb=" N ILE B 118 " pdb=" CA ILE B 118 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.75e+00 ... (remaining 4529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 5594 1.64 - 3.28: 520 3.28 - 4.92: 45 4.92 - 6.56: 3 6.56 - 8.20: 4 Bond angle restraints: 6166 Sorted by residual: angle pdb=" N LYS B 58 " pdb=" CA LYS B 58 " pdb=" C LYS B 58 " ideal model delta sigma weight residual 113.97 105.77 8.20 1.28e+00 6.10e-01 4.11e+01 angle pdb=" C GLU B 116 " pdb=" N GLU B 117 " pdb=" CA GLU B 117 " ideal model delta sigma weight residual 122.08 127.61 -5.53 1.47e+00 4.63e-01 1.41e+01 angle pdb=" CA GLY A 193 " pdb=" C GLY A 193 " pdb=" O GLY A 193 " ideal model delta sigma weight residual 121.18 117.99 3.19 8.80e-01 1.29e+00 1.31e+01 angle pdb=" N LEU B 60 " pdb=" CA LEU B 60 " pdb=" C LEU B 60 " ideal model delta sigma weight residual 113.19 108.99 4.20 1.19e+00 7.06e-01 1.24e+01 angle pdb=" CA THR B 57 " pdb=" CB THR B 57 " pdb=" OG1 THR B 57 " ideal model delta sigma weight residual 109.60 104.67 4.93 1.50e+00 4.44e-01 1.08e+01 ... (remaining 6161 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 2437 17.14 - 34.29: 248 34.29 - 51.43: 70 51.43 - 68.58: 33 68.58 - 85.72: 6 Dihedral angle restraints: 2794 sinusoidal: 1189 harmonic: 1605 Sorted by residual: dihedral pdb=" CB CYS B 175 " pdb=" SG CYS B 175 " pdb=" SG CYS B 197 " pdb=" CB CYS B 197 " ideal model delta sinusoidal sigma weight residual 93.00 57.98 35.02 1 1.00e+01 1.00e-02 1.74e+01 dihedral pdb=" CB CYS B 66 " pdb=" SG CYS B 66 " pdb=" SG CYS B 130 " pdb=" CB CYS B 130 " ideal model delta sinusoidal sigma weight residual 93.00 124.92 -31.92 1 1.00e+01 1.00e-02 1.45e+01 dihedral pdb=" CB CYS C 38 " pdb=" SG CYS C 38 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -117.68 31.68 1 1.00e+01 1.00e-02 1.43e+01 ... (remaining 2791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 654 0.129 - 0.258: 29 0.258 - 0.387: 0 0.387 - 0.516: 0 0.516 - 0.645: 1 Chirality restraints: 684 Sorted by residual: chirality pdb=" CG LEU C 42 " pdb=" CB LEU C 42 " pdb=" CD1 LEU C 42 " pdb=" CD2 LEU C 42 " both_signs ideal model delta sigma weight residual False -2.59 -1.94 -0.65 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" CA ARG A 28 " pdb=" N ARG A 28 " pdb=" C ARG A 28 " pdb=" CB ARG A 28 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ILE C 96 " pdb=" N ILE C 96 " pdb=" C ILE C 96 " pdb=" CB ILE C 96 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.41e-01 ... (remaining 681 not shown) Planarity restraints: 792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 39 " 0.234 9.50e-02 1.11e+02 1.05e-01 6.76e+00 pdb=" NE ARG C 39 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG C 39 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 39 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 39 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 151 " -0.229 9.50e-02 1.11e+02 1.03e-01 6.47e+00 pdb=" NE ARG C 151 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 151 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 151 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 151 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 88 " 0.214 9.50e-02 1.11e+02 9.59e-02 5.63e+00 pdb=" NE ARG A 88 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 88 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 88 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 88 " 0.008 2.00e-02 2.50e+03 ... (remaining 789 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 334 2.74 - 3.28: 4160 3.28 - 3.82: 7244 3.82 - 4.36: 8868 4.36 - 4.90: 15059 Nonbonded interactions: 35665 Sorted by model distance: nonbonded pdb=" OH TYR B 39 " pdb=" O LYS B 68 " model vdw 2.205 3.040 nonbonded pdb=" OD2 ASP B 71 " pdb=" NH1 ARG C 147 " model vdw 2.244 3.120 nonbonded pdb=" NH2 ARG A 130 " pdb=" O GLN B 163 " model vdw 2.249 3.120 nonbonded pdb=" O VAL A 108 " pdb=" OH TYR A 149 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR B 125 " pdb=" OG1 THR B 180 " model vdw 2.293 3.040 ... (remaining 35660 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.070 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 4534 Z= 0.450 Angle : 0.922 8.202 6166 Z= 0.647 Chirality : 0.063 0.645 684 Planarity : 0.009 0.105 790 Dihedral : 16.577 85.720 1722 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.61 % Allowed : 20.33 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.37), residues: 534 helix: 1.47 (0.50), residues: 117 sheet: 0.83 (0.39), residues: 181 loop : -0.41 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 91 HIS 0.006 0.001 HIS C 95 PHE 0.006 0.001 PHE C 43 TYR 0.009 0.001 TYR A 59 ARG 0.005 0.001 ARG C 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.454 Fit side-chains REVERT: A 160 LYS cc_start: 0.8039 (tttt) cc_final: 0.7760 (ttmt) REVERT: A 182 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7729 (mp0) REVERT: B 117 GLU cc_start: 0.6923 (pt0) cc_final: 0.6610 (pt0) REVERT: B 172 GLU cc_start: 0.5330 (mt-10) cc_final: 0.4660 (tt0) REVERT: B 191 LYS cc_start: 0.8053 (pttp) cc_final: 0.7798 (pttp) REVERT: C 64 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7354 (mt-10) outliers start: 3 outliers final: 2 residues processed: 87 average time/residue: 1.2193 time to fit residues: 109.9404 Evaluate side-chains 74 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain C residue 42 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN C 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.145086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.118499 restraints weight = 5037.655| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.17 r_work: 0.3142 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4534 Z= 0.217 Angle : 0.595 10.182 6166 Z= 0.293 Chirality : 0.042 0.175 684 Planarity : 0.005 0.046 790 Dihedral : 5.210 47.994 632 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.85 % Allowed : 19.51 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.37), residues: 534 helix: 1.46 (0.48), residues: 131 sheet: 0.85 (0.38), residues: 181 loop : -0.28 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 100 HIS 0.003 0.001 HIS A 97 PHE 0.030 0.002 PHE C 43 TYR 0.012 0.001 TYR B 20 ARG 0.007 0.001 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 GLU cc_start: 0.8199 (tt0) cc_final: 0.7803 (pt0) REVERT: A 123 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7870 (tp) REVERT: A 160 LYS cc_start: 0.8267 (tttt) cc_final: 0.7926 (ttmp) REVERT: A 182 GLU cc_start: 0.8488 (mt-10) cc_final: 0.7963 (mp0) REVERT: B 117 GLU cc_start: 0.7259 (pt0) cc_final: 0.7000 (mm-30) REVERT: B 172 GLU cc_start: 0.5474 (mt-10) cc_final: 0.4873 (tt0) REVERT: B 191 LYS cc_start: 0.8770 (pttp) cc_final: 0.8538 (pttp) REVERT: C 64 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8150 (mt-10) outliers start: 14 outliers final: 6 residues processed: 80 average time/residue: 1.0764 time to fit residues: 89.7521 Evaluate side-chains 75 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 123 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 97 HIS ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN B 160 GLN C 126 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.146576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.121178 restraints weight = 5065.701| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.06 r_work: 0.3079 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4534 Z= 0.264 Angle : 0.599 10.941 6166 Z= 0.296 Chirality : 0.043 0.167 684 Planarity : 0.005 0.036 790 Dihedral : 4.314 15.321 630 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.86 % Allowed : 18.70 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.37), residues: 534 helix: 1.25 (0.47), residues: 131 sheet: 0.86 (0.39), residues: 176 loop : -0.40 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 100 HIS 0.003 0.001 HIS A 97 PHE 0.010 0.002 PHE B 142 TYR 0.011 0.001 TYR A 140 ARG 0.006 0.001 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7926 (tp) REVERT: A 148 MET cc_start: 0.9118 (tpt) cc_final: 0.8894 (tpt) REVERT: A 160 LYS cc_start: 0.8286 (tttt) cc_final: 0.7959 (ttmp) REVERT: A 182 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8005 (mp0) REVERT: A 206 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7804 (tm-30) REVERT: B 117 GLU cc_start: 0.7338 (pt0) cc_final: 0.7066 (mm-30) REVERT: B 138 TYR cc_start: 0.8937 (p90) cc_final: 0.8657 (p90) REVERT: B 166 LEU cc_start: 0.8843 (mt) cc_final: 0.8497 (mp) REVERT: B 172 GLU cc_start: 0.5655 (mt-10) cc_final: 0.5080 (tt0) REVERT: B 191 LYS cc_start: 0.8771 (pttp) cc_final: 0.8204 (mmmt) REVERT: C 43 PHE cc_start: 0.6953 (OUTLIER) cc_final: 0.5649 (t80) REVERT: C 64 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8285 (mt-10) outliers start: 19 outliers final: 9 residues processed: 80 average time/residue: 1.1378 time to fit residues: 94.5414 Evaluate side-chains 77 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 123 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 157 GLN B 149 ASN C 126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.141695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.116264 restraints weight = 5065.317| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.07 r_work: 0.3029 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4534 Z= 0.302 Angle : 0.607 11.631 6166 Z= 0.301 Chirality : 0.043 0.173 684 Planarity : 0.005 0.037 790 Dihedral : 4.393 15.609 630 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.86 % Allowed : 19.31 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.37), residues: 534 helix: 1.28 (0.48), residues: 124 sheet: 0.77 (0.39), residues: 176 loop : -0.45 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 100 HIS 0.003 0.001 HIS A 97 PHE 0.012 0.002 PHE C 43 TYR 0.013 0.001 TYR B 20 ARG 0.005 0.001 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.9079 (tpt) cc_final: 0.8850 (tpt) REVERT: A 160 LYS cc_start: 0.8286 (tttt) cc_final: 0.7946 (ttmp) REVERT: A 178 LEU cc_start: 0.8705 (mt) cc_final: 0.8461 (mp) REVERT: A 182 GLU cc_start: 0.8529 (mt-10) cc_final: 0.7971 (mp0) REVERT: A 206 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7794 (tm-30) REVERT: B 138 TYR cc_start: 0.8958 (p90) cc_final: 0.8670 (p90) REVERT: B 166 LEU cc_start: 0.8818 (mt) cc_final: 0.8487 (mp) REVERT: B 191 LYS cc_start: 0.8752 (pttp) cc_final: 0.8135 (mmmt) REVERT: C 43 PHE cc_start: 0.7035 (OUTLIER) cc_final: 0.5694 (t80) REVERT: C 64 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8216 (mt-10) outliers start: 19 outliers final: 9 residues processed: 84 average time/residue: 1.2020 time to fit residues: 104.9926 Evaluate side-chains 80 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 123 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 49 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 27 optimal weight: 0.0370 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 149 ASN C 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.145468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.119812 restraints weight = 5094.173| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.10 r_work: 0.3142 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4534 Z= 0.245 Angle : 0.573 7.489 6166 Z= 0.288 Chirality : 0.042 0.212 684 Planarity : 0.004 0.032 790 Dihedral : 4.263 15.820 628 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.05 % Allowed : 21.34 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.37), residues: 534 helix: 1.54 (0.49), residues: 120 sheet: 0.75 (0.39), residues: 176 loop : -0.47 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 100 HIS 0.003 0.001 HIS A 97 PHE 0.014 0.001 PHE C 43 TYR 0.013 0.001 TYR B 20 ARG 0.005 0.001 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 LYS cc_start: 0.8337 (tttt) cc_final: 0.8018 (ttmp) REVERT: A 178 LEU cc_start: 0.8717 (mt) cc_final: 0.8511 (mp) REVERT: A 182 GLU cc_start: 0.8517 (mt-10) cc_final: 0.7983 (mp0) REVERT: B 53 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7638 (pt0) REVERT: B 166 LEU cc_start: 0.8831 (mt) cc_final: 0.8495 (mp) REVERT: B 191 LYS cc_start: 0.8745 (pttp) cc_final: 0.8192 (mmmt) REVERT: C 43 PHE cc_start: 0.6931 (OUTLIER) cc_final: 0.5621 (t80) REVERT: C 64 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8177 (mt-10) outliers start: 15 outliers final: 7 residues processed: 83 average time/residue: 1.0958 time to fit residues: 94.6439 Evaluate side-chains 75 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 123 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 1 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 50 optimal weight: 0.0770 chunk 32 optimal weight: 0.6980 chunk 42 optimal weight: 0.0470 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 149 ASN C 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.141981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.116029 restraints weight = 5018.369| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.16 r_work: 0.3071 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4534 Z= 0.156 Angle : 0.533 7.089 6166 Z= 0.267 Chirality : 0.040 0.165 684 Planarity : 0.004 0.032 790 Dihedral : 4.072 15.590 628 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.85 % Allowed : 22.56 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.37), residues: 534 helix: 1.72 (0.49), residues: 120 sheet: 0.90 (0.39), residues: 175 loop : -0.38 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 100 HIS 0.003 0.000 HIS A 97 PHE 0.008 0.001 PHE C 43 TYR 0.014 0.001 TYR B 20 ARG 0.004 0.000 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.8224 (tpp) cc_final: 0.7903 (mmm) REVERT: A 160 LYS cc_start: 0.8359 (tttt) cc_final: 0.8013 (ttmp) REVERT: A 182 GLU cc_start: 0.8516 (mt-10) cc_final: 0.7928 (mp0) REVERT: A 206 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7789 (tm-30) REVERT: B 166 LEU cc_start: 0.8798 (mt) cc_final: 0.8445 (mp) REVERT: B 191 LYS cc_start: 0.8723 (pttp) cc_final: 0.8137 (mmmt) REVERT: C 43 PHE cc_start: 0.6758 (OUTLIER) cc_final: 0.5377 (t80) REVERT: C 64 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8107 (mt-10) outliers start: 14 outliers final: 5 residues processed: 81 average time/residue: 2.0739 time to fit residues: 174.7159 Evaluate side-chains 69 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 123 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 32 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 149 ASN C 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.145893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.120916 restraints weight = 5010.142| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.05 r_work: 0.3087 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4534 Z= 0.189 Angle : 0.547 6.915 6166 Z= 0.272 Chirality : 0.041 0.145 684 Planarity : 0.004 0.034 790 Dihedral : 4.040 14.737 628 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.03 % Allowed : 23.98 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.37), residues: 534 helix: 1.81 (0.49), residues: 120 sheet: 0.90 (0.39), residues: 175 loop : -0.35 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 100 HIS 0.003 0.001 HIS A 97 PHE 0.009 0.001 PHE C 43 TYR 0.009 0.001 TYR B 138 ARG 0.005 0.000 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.8179 (tpp) cc_final: 0.7881 (mmm) REVERT: A 160 LYS cc_start: 0.8346 (tttt) cc_final: 0.8028 (ttmp) REVERT: A 182 GLU cc_start: 0.8514 (mt-10) cc_final: 0.7989 (mp0) REVERT: A 206 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7793 (tm-30) REVERT: B 166 LEU cc_start: 0.8816 (mt) cc_final: 0.8463 (mp) REVERT: B 191 LYS cc_start: 0.8713 (pttp) cc_final: 0.8178 (mmmt) REVERT: C 43 PHE cc_start: 0.6916 (OUTLIER) cc_final: 0.5497 (t80) REVERT: C 64 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8040 (mt-10) outliers start: 10 outliers final: 5 residues processed: 71 average time/residue: 2.1465 time to fit residues: 157.7609 Evaluate side-chains 68 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 123 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 45 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS C 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.146675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.122014 restraints weight = 5024.157| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.03 r_work: 0.3100 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4534 Z= 0.193 Angle : 0.544 6.943 6166 Z= 0.271 Chirality : 0.041 0.144 684 Planarity : 0.004 0.034 790 Dihedral : 4.050 15.784 628 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.44 % Allowed : 23.37 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.36), residues: 534 helix: 1.86 (0.49), residues: 120 sheet: 0.86 (0.39), residues: 175 loop : -0.35 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 100 HIS 0.004 0.001 HIS A 97 PHE 0.010 0.001 PHE C 43 TYR 0.013 0.001 TYR B 20 ARG 0.005 0.000 ARG C 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 LYS cc_start: 0.8798 (ttpp) cc_final: 0.8493 (tttt) REVERT: A 160 LYS cc_start: 0.8354 (tttt) cc_final: 0.8034 (ttmp) REVERT: A 182 GLU cc_start: 0.8536 (mt-10) cc_final: 0.7972 (mp0) REVERT: A 206 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7787 (tm-30) REVERT: B 166 LEU cc_start: 0.8823 (mt) cc_final: 0.8462 (mp) REVERT: B 191 LYS cc_start: 0.8708 (pttp) cc_final: 0.8178 (mmmt) REVERT: C 43 PHE cc_start: 0.6919 (OUTLIER) cc_final: 0.5632 (t80) REVERT: C 64 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8042 (mt-10) outliers start: 12 outliers final: 6 residues processed: 72 average time/residue: 1.1815 time to fit residues: 88.3613 Evaluate side-chains 69 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 65 MET Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 123 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 13 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS C 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.134564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.107962 restraints weight = 5107.791| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.21 r_work: 0.2997 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 4534 Z= 0.367 Angle : 0.634 7.664 6166 Z= 0.320 Chirality : 0.044 0.189 684 Planarity : 0.004 0.035 790 Dihedral : 4.430 17.352 628 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.64 % Allowed : 23.37 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.36), residues: 534 helix: 1.28 (0.48), residues: 124 sheet: 0.55 (0.37), residues: 180 loop : -0.44 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 100 HIS 0.003 0.001 HIS A 97 PHE 0.018 0.002 PHE C 43 TYR 0.015 0.002 TYR B 20 ARG 0.003 0.001 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 146 LYS cc_start: 0.8779 (ttpp) cc_final: 0.8493 (tttt) REVERT: A 160 LYS cc_start: 0.8290 (tttt) cc_final: 0.7913 (ttmp) REVERT: A 178 LEU cc_start: 0.8755 (mt) cc_final: 0.8531 (mp) REVERT: A 182 GLU cc_start: 0.8565 (mt-10) cc_final: 0.7802 (mp0) REVERT: A 206 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7792 (tm-30) REVERT: B 166 LEU cc_start: 0.8816 (mt) cc_final: 0.8438 (mp) REVERT: B 191 LYS cc_start: 0.8703 (pttp) cc_final: 0.8081 (mmmt) REVERT: C 43 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.6224 (t80) REVERT: C 64 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8208 (mt-10) outliers start: 13 outliers final: 7 residues processed: 74 average time/residue: 1.4225 time to fit residues: 109.0995 Evaluate side-chains 78 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 123 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 34 optimal weight: 0.0050 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 25 optimal weight: 0.0870 chunk 47 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 43 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.3172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS C 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.138455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.112164 restraints weight = 5058.758| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.20 r_work: 0.3059 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4534 Z= 0.167 Angle : 0.550 7.322 6166 Z= 0.275 Chirality : 0.040 0.136 684 Planarity : 0.004 0.032 790 Dihedral : 4.161 15.534 628 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.22 % Allowed : 25.00 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.37), residues: 534 helix: 1.79 (0.49), residues: 120 sheet: 0.72 (0.38), residues: 178 loop : -0.35 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 100 HIS 0.005 0.001 HIS A 97 PHE 0.008 0.001 PHE C 43 TYR 0.016 0.001 TYR B 20 ARG 0.003 0.000 ARG A 88 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1068 Ramachandran restraints generated. 534 Oldfield, 0 Emsley, 534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 108 VAL cc_start: 0.8521 (t) cc_final: 0.8075 (p) REVERT: A 146 LYS cc_start: 0.8813 (ttpp) cc_final: 0.8497 (tttt) REVERT: A 160 LYS cc_start: 0.8243 (tttt) cc_final: 0.7895 (ttmp) REVERT: A 178 LEU cc_start: 0.8737 (mt) cc_final: 0.8504 (mp) REVERT: A 182 GLU cc_start: 0.8515 (mt-10) cc_final: 0.7894 (mp0) REVERT: A 206 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7783 (tm-30) REVERT: B 138 TYR cc_start: 0.8990 (p90) cc_final: 0.8744 (p90) REVERT: B 166 LEU cc_start: 0.8800 (mt) cc_final: 0.8428 (mp) REVERT: B 191 LYS cc_start: 0.8709 (pttp) cc_final: 0.8131 (mmmt) REVERT: C 43 PHE cc_start: 0.7024 (OUTLIER) cc_final: 0.5709 (t80) REVERT: C 64 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8107 (mt-10) outliers start: 6 outliers final: 3 residues processed: 73 average time/residue: 1.1889 time to fit residues: 90.1620 Evaluate side-chains 71 residues out of total 492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 123 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 38 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS C 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.145709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.120709 restraints weight = 5043.013| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.08 r_work: 0.3069 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4534 Z= 0.204 Angle : 0.563 8.609 6166 Z= 0.280 Chirality : 0.041 0.147 684 Planarity : 0.004 0.034 790 Dihedral : 4.179 17.696 628 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.22 % Allowed : 25.41 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.37), residues: 534 helix: 1.84 (0.49), residues: 120 sheet: 0.82 (0.39), residues: 167 loop : -0.40 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 100 HIS 0.004 0.001 HIS A 97 PHE 0.010 0.001 PHE C 43 TYR 0.016 0.001 TYR B 20 ARG 0.002 0.000 ARG C 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3885.97 seconds wall clock time: 69 minutes 52.33 seconds (4192.33 seconds total)